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root/OpenMD/trunk/src/visitors/AtomVisitor.cpp
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Comparing trunk/src/visitors/AtomVisitor.cpp (file contents):
Revision 413 by tim, Wed Mar 9 17:30:29 2005 UTC vs.
Revision 1244 by xsun, Wed May 14 21:04:13 2008 UTC

# Line 1 | Line 1
1 < /*
1 > /*
2   * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3   *
4   * The University of Notre Dame grants you ("Licensee") a
# Line 45 | Line 45 | namespace oopse {
45   #include "primitives/RigidBody.hpp"
46  
47   namespace oopse {
48 < void BaseAtomVisitor::visit(RigidBody *rb) {
49 < //vector<Atom*> myAtoms;
50 < //vector<Atom*>::iterator atomIter;
48 >  void BaseAtomVisitor::visit(RigidBody *rb) {
49 >    //vector<Atom*> myAtoms;
50 >    //vector<Atom*>::iterator atomIter;
51  
52 < //myAtoms = rb->getAtoms();
52 >    //myAtoms = rb->getAtoms();
53  
54 < //for(atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter)
55 < //  (*atomIter)->accept(this);
56 <    }
54 >    //for(atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter)
55 >    //  (*atomIter)->accept(this);
56 >  }
57  
58 < void BaseAtomVisitor::setVisited(Atom *atom) {
58 >  void BaseAtomVisitor::setVisited(Atom *atom) {
59      GenericData *data;
60      data = atom->getPropertyByName("VISITED");
61  
62      //if visited property is not existed, add it as new property
63      if (data == NULL) {
64 <        data = new GenericData();
65 <        data->setID("VISITED");
66 <        atom->addProperty(data);
64 >      data = new GenericData();
65 >      data->setID("VISITED");
66 >      atom->addProperty(data);
67      }
68 < }
68 >  }
69  
70 < bool BaseAtomVisitor::isVisited(Atom *atom) {
70 >  bool BaseAtomVisitor::isVisited(Atom *atom) {
71      GenericData *data;
72      data = atom->getPropertyByName("VISITED");
73      return data == NULL ? false : true;
74 < }
74 >  }
75  
76 < bool SSDAtomVisitor::isSSDAtom(const std::string&atomType) {
76 >  bool SSDAtomVisitor::isSSDAtom(const std::string&atomType) {
77      std::set<std::string>::iterator strIter;
78      strIter = ssdAtomType.find(atomType);
79      return strIter != ssdAtomType.end() ? true : false;
80 < }
80 >  }
81  
82 < void SSDAtomVisitor::visit(DirectionalAtom *datom) {
82 >  void SSDAtomVisitor::visit(DirectionalAtom *datom) {
83      std::vector<AtomInfo*>atoms;
84  
85 <    //we need to convert SSD into 4 differnet atoms
86 <    //one oxygen atom, two hydrogen atoms and one pseudo atom which is the center of the mass
87 <    //of the water with a dipole moment
85 >    //we need to convert SSD into 4 different atoms
86 >    //one oxygen atom, two hydrogen atoms and one pseudo atom which is the center of
87 >    //the mass of the water with a dipole moment
88      Vector3d h1(0.0, -0.75695, 0.5206);
89      Vector3d h2(0.0, 0.75695, 0.5206);
90      Vector3d ox(0.0, 0.0, -0.0654);
# Line 101 | Line 101 | void SSDAtomVisitor::visit(DirectionalAtom *datom) {
101  
102      //if atom is not SSD atom, just skip it
103      if (!isSSDAtom(datom->getType()))
104 <        return;
104 >      return;
105  
106      data = datom->getPropertyByName("ATOMDATA");
107  
108      if (data != NULL) {
109 <        atomData = dynamic_cast<AtomData *>(data);
109 >      atomData = dynamic_cast<AtomData *>(data);
110  
111 <        if (atomData == NULL) {
112 <            std::cerr << "can not get Atom Data from " << datom->getType() << std::endl;
113 <            atomData = new AtomData;
114 <            haveAtomData = false;
115 <        } else
116 <            haveAtomData = true;
111 >      if (atomData == NULL) {
112 >        std::cerr << "can not get Atom Data from " << datom->getType() << std::endl;
113 >        atomData = new AtomData;
114 >        haveAtomData = false;
115 >      } else
116 >        haveAtomData = true;
117      } else {
118 <        atomData = new AtomData;
119 <        haveAtomData = false;
118 >      atomData = new AtomData;
119 >      haveAtomData = false;
120      }
121  
122      pos = datom->getPos();
# Line 185 | Line 185 | void SSDAtomVisitor::visit(DirectionalAtom *datom) {
185      //add atom data into atom's property
186  
187      if (!haveAtomData) {
188 <        atomData->setID("ATOMDATA");
189 <        datom->addProperty(atomData);
188 >      atomData->setID("ATOMDATA");
189 >      datom->addProperty(atomData);
190      }
191  
192      setVisited(datom);
193 < }
193 >  }
194  
195 < const std::string SSDAtomVisitor::toString() {
195 >  const std::string SSDAtomVisitor::toString() {
196      char   buffer[65535];
197      std::string result;
198  
# Line 212 | Line 212 | const std::string SSDAtomVisitor::toString() {
212      result += buffer;
213  
214      return result;
215 < }
215 >  }
216  
217 < bool LinearAtomVisitor::isLinearAtom(const std::string& atomType){
217 >
218 >  bool TREDAtomVisitor::isTREDAtom(const std::string&atomType) {
219      std::set<std::string>::iterator strIter;
220 +    strIter = tredAtomType.find(atomType);
221 +    return strIter != tredAtomType.end() ? true : false;
222 +  }
223 +
224 +  void TREDAtomVisitor::visit(DirectionalAtom *datom) {
225 +    std::vector<AtomInfo*>atoms;
226 +
227 +    // we need to convert a TRED into 4 different atoms:
228 +    // one oxygen atom, two hydrogen atoms, and one atom which is the center of
229 +    // the mass of the water with a dipole moment
230 +    Vector3d h1(0.0, -0.75695, 0.5206);
231 +    Vector3d h2(0.0, 0.75695, 0.5206);
232 +    Vector3d ox(0.0, 0.0, -0.0654);
233 +    Vector3d u(0, 0, 1);
234 +    RotMat3x3d   rotMatrix;
235 +    RotMat3x3d   rotTrans;
236 +    AtomInfo *   atomInfo;
237 +    Vector3d     pos;
238 +    Vector3d     newVec;
239 +    Quat4d       q;
240 +    AtomData *   atomData;
241 +    GenericData *data;
242 +    bool         haveAtomData;
243 +
244 +    // if the atom is not a TRED atom, skip it
245 +    if (!isTREDAtom(datom->getType()))
246 +      return;
247 +
248 +    data = datom->getPropertyByName("ATOMDATA");
249 +
250 +    if (data != NULL) {
251 +      atomData = dynamic_cast<AtomData *>(data);
252 +
253 +      if (atomData == NULL) {
254 +        std::cerr << "can not get Atom Data from " << datom->getType() << std::endl;
255 +        atomData = new AtomData;
256 +        haveAtomData = false;
257 +      } else
258 +        haveAtomData = true;
259 +    } else {
260 +      atomData = new AtomData;
261 +      haveAtomData = false;
262 +    }
263 +
264 +    pos = datom->getPos();
265 +    q = datom->getQ();
266 +    rotMatrix = datom->getA();
267 +
268 +    // We need A^T to convert from body-fixed to space-fixed:
269 +    // transposeMat3(rotMatrix, rotTrans);
270 +    rotTrans = rotMatrix.transpose();
271 +
272 +    // center of mass of the water molecule
273 +    // matVecMul3(rotTrans, u, newVec);
274 +    newVec = rotTrans * u;
275 +
276 +    atomInfo = new AtomInfo;
277 +    atomInfo->atomTypeName = "TRED";
278 +    atomInfo->pos[0] = pos[0];
279 +    atomInfo->pos[1] = pos[1];
280 +    atomInfo->pos[2] = pos[2];
281 +    atomInfo->dipole[0] = newVec[0];
282 +    atomInfo->dipole[1] = newVec[1];
283 +    atomInfo->dipole[2] = newVec[2];
284 +
285 +    atomData->addAtomInfo(atomInfo);
286 +
287 +    // oxygen
288 +    // matVecMul3(rotTrans, ox, newVec);
289 +    newVec = rotTrans * ox;
290 +
291 +    atomInfo = new AtomInfo;
292 +    atomInfo->atomTypeName = "O";
293 +    atomInfo->pos[0] = pos[0] + newVec[0];
294 +    atomInfo->pos[1] = pos[1] + newVec[1];
295 +    atomInfo->pos[2] = pos[2] + newVec[2];
296 +    atomInfo->dipole[0] = 0.0;
297 +    atomInfo->dipole[1] = 0.0;
298 +    atomInfo->dipole[2] = 0.0;
299 +    atomData->addAtomInfo(atomInfo);
300 +
301 +    // hydrogen1
302 +    // matVecMul3(rotTrans, h1, newVec);
303 +    newVec = rotTrans * h1;
304 +    atomInfo = new AtomInfo;
305 +    atomInfo->atomTypeName = "H";
306 +    atomInfo->pos[0] = pos[0] + newVec[0];
307 +    atomInfo->pos[1] = pos[1] + newVec[1];
308 +    atomInfo->pos[2] = pos[2] + newVec[2];
309 +    atomInfo->dipole[0] = 0.0;
310 +    atomInfo->dipole[1] = 0.0;
311 +    atomInfo->dipole[2] = 0.0;
312 +    atomData->addAtomInfo(atomInfo);
313 +
314 +    // hydrogen2
315 +    // matVecMul3(rotTrans, h2, newVec);
316 +    newVec = rotTrans * h2;
317 +    atomInfo = new AtomInfo;
318 +    atomInfo->atomTypeName = "H";
319 +    atomInfo->pos[0] = pos[0] + newVec[0];
320 +    atomInfo->pos[1] = pos[1] + newVec[1];
321 +    atomInfo->pos[2] = pos[2] + newVec[2];
322 +    atomInfo->dipole[0] = 0.0;
323 +    atomInfo->dipole[1] = 0.0;
324 +    atomInfo->dipole[2] = 0.0;
325 +    atomData->addAtomInfo(atomInfo);
326 +
327 +    // add atom data into atom's property
328 +
329 +    if (!haveAtomData) {
330 +      atomData->setID("ATOMDATA");
331 +      datom->addProperty(atomData);
332 +    }
333 +
334 +    setVisited(datom);
335 +  }
336 +
337 +  const std::string TREDAtomVisitor::toString() {
338 +    char   buffer[65535];
339 +    std::string result;
340 +
341 +    sprintf(buffer,
342 +            "------------------------------------------------------------------\n");
343 +    result += buffer;
344 +
345 +    sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
346 +    result += buffer;
347 +
348 +    sprintf(buffer,
349 +            "Visitor Description: Convert the TRED atom into 4 different atoms\n");
350 +    result += buffer;
351 +
352 +    sprintf(buffer,
353 +            "------------------------------------------------------------------\n");
354 +    result += buffer;
355 +
356 +    return result;
357 +  }
358 +
359 +
360 +  bool LinearAtomVisitor::isLinearAtom(const std::string& atomType){
361 +    std::set<std::string>::iterator strIter;
362      strIter = linearAtomType.find(atomType);
363  
364      return strIter != linearAtomType.end() ? true : false;
365 < }
365 >  }
366  
367 < void LinearAtomVisitor::visit(DirectionalAtom* datom){
367 >  void LinearAtomVisitor::addGayBerneAtomType(const std::string& atomType){
368 >   linearAtomType.insert(atomType);
369 >  }
370 >
371 >  void LinearAtomVisitor::visit(DirectionalAtom* datom){
372      std::vector<AtomInfo*> atoms;
373      //we need to convert linear into 4 different atoms
374      Vector3d c1(0.0, 0.0, -1.8);
# Line 237 | Line 384 | void LinearAtomVisitor::visit(DirectionalAtom* datom){
384      AtomData* atomData;
385      GenericData* data;
386      bool haveAtomData;
387 +    AtomType* atomType;
388 +    //if atom is not linear atom, just skip it
389 +    if(!isLinearAtom(datom->getType()) || !datom->getAtomType()->isGayBerne())
390 +      return;
391  
392 <    //if atom is not SSD atom, just skip it
393 <    if(!isLinearAtom(datom->getType()))
394 <        return;
392 >    //setup GayBerne type in fortran side
393 >    data = datom->getAtomType()->getPropertyByName("GayBerne");
394 >    if (data != NULL) {
395 >       GayBerneParamGenericData* gayBerneData = dynamic_cast<GayBerneParamGenericData*>(data);
396  
397 +       if (gayBerneData != NULL) {
398 +           GayBerneParam gayBerneParam = gayBerneData->getData();
399 +
400 +                          // double halfLen = gayBerneParam.GB_sigma * gayBerneParam.GB_l2b_ratio/2.0;
401 +                          double halfLen = gayBerneParam.GB_l/2.0;
402 +                          c1[2] = -halfLen;
403 +              c2[2] = -halfLen /2;
404 +              c3[2] = halfLen/2;
405 +              c4[2] = halfLen;
406 +                
407 +            }
408 +            
409 +              else {
410 +                    sprintf( painCave.errMsg,
411 +                           "Can not cast GenericData to GayBerneParam\n");
412 +                    painCave.severity = OOPSE_ERROR;
413 +                    painCave.isFatal = 1;
414 +                    simError();          
415 +        }            
416 +    }
417 +
418 +
419      data = datom->getPropertyByName("ATOMDATA");
420      if(data != NULL){
421 <        atomData = dynamic_cast<AtomData*>(data);  
422 <        if(atomData == NULL){
423 <            std::cerr << "can not get Atom Data from " << datom->getType() << std::endl;
424 <            atomData = new AtomData;
425 <            haveAtomData = false;      
426 <        } else {
427 <            haveAtomData = true;
428 <        }
421 >      atomData = dynamic_cast<AtomData*>(data);  
422 >      if(atomData == NULL){
423 >        std::cerr << "can not get Atom Data from " << datom->getType() << std::endl;
424 >        atomData = new AtomData;
425 >        haveAtomData = false;      
426 >      } else {
427 >        haveAtomData = true;
428 >      }
429      } else {
430 <        atomData = new AtomData;
431 <        haveAtomData = false;
430 >      atomData = new AtomData;
431 >      haveAtomData = false;
432      }
433    
434    
# Line 312 | Line 486 | void LinearAtomVisitor::visit(DirectionalAtom* datom){
486      //add atom data into atom's property
487  
488      if(!haveAtomData){
489 <        atomData->setID("ATOMDATA");
490 <        datom->addProperty(atomData);
489 >      atomData->setID("ATOMDATA");
490 >      datom->addProperty(atomData);
491      }
492  
493      setVisited(datom);
494  
495 < }
495 >  }
496  
497 < const std::string LinearAtomVisitor::toString(){
498 <  char buffer[65535];
499 <  std::string result;
497 >  const std::string LinearAtomVisitor::toString(){
498 >    char buffer[65535];
499 >    std::string result;
500    
501 <  sprintf(buffer ,"------------------------------------------------------------------\n");
502 <  result += buffer;
501 >    sprintf(buffer ,"------------------------------------------------------------------\n");
502 >    result += buffer;
503  
504 <  sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
505 <  result += buffer;
504 >    sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
505 >    result += buffer;
506  
507 <  sprintf(buffer , "Visitor Description: Convert linear into 4 different atoms\n");
508 <  result += buffer;
507 >    sprintf(buffer , "Visitor Description: Convert linear into 4 different atoms\n");
508 >    result += buffer;
509  
510 <  sprintf(buffer ,"------------------------------------------------------------------\n");
511 <  result += buffer;
510 >    sprintf(buffer ,"------------------------------------------------------------------\n");
511 >    result += buffer;
512  
513 <  return result;
514 < }
513 >    return result;
514 >  }
515  
516 < //----------------------------------------------------------------------------//
516 >  bool GBLipidAtomVisitor::isGBLipidAtom(const std::string& atomType){
517 >    std::set<std::string>::iterator strIter;
518 >    strIter = GBLipidAtomType.find(atomType);
519  
520 < void DefaultAtomVisitor::visit(Atom *atom) {
520 >    return strIter != GBLipidAtomType.end() ? true : false;
521 >  }
522 >
523 >  void GBLipidAtomVisitor::visit(DirectionalAtom* datom){
524 >    std::vector<AtomInfo*> atoms;
525 >    Vector3d c1(0.0, 0.0, 0.0);
526 >    Vector3d c2(0.0, 0.0, 1.0);
527 >    RotMat3x3d rotMatrix;
528 >    RotMat3x3d rotTrans;
529 >    AtomInfo* atomInfo;
530 >    Vector3d pos;
531 >    Vector3d newVec;
532 >    Vector3d dVec;
533 >    Quat4d q;
534 >    AtomData* atomData;
535 >    GenericData* data;
536 >    bool haveAtomData;
537 >
538 >    //if atom is not GBlipid atom, just skip it
539 >    if(!isGBLipidAtom(datom->getType()))
540 >      return;
541 >
542 >    data = datom->getPropertyByName("ATOMDATA");
543 >    if(data != NULL){
544 >      atomData = dynamic_cast<AtomData*>(data);  
545 >      if(atomData == NULL){
546 >        std::cerr << "can not get Atom Data from " << datom->getType() << std::endl;
547 >        atomData = new AtomData;
548 >        haveAtomData = false;      
549 >      } else {
550 >        haveAtomData = true;
551 >      }
552 >    } else {
553 >      atomData = new AtomData;
554 >      haveAtomData = false;
555 >    }
556 >  
557 >  
558 >    pos = datom->getPos();
559 >    q = datom->getQ();
560 >    rotMatrix = datom->getA();
561 >
562 >    // We need A^T to convert from body-fixed to space-fixed:  
563 >    rotTrans = rotMatrix.transpose();
564 >
565 >    newVec = rotTrans * c1;
566 >    dVec = rotTrans * c2;
567 >    atomInfo = new AtomInfo;
568 >    atomInfo->atomTypeName = "GB";
569 >    atomInfo->pos[0] = pos[0] + newVec[0];
570 >    atomInfo->pos[1] = pos[1] + newVec[1];
571 >    atomInfo->pos[2] = pos[2] + newVec[2];
572 >    atomInfo->dipole[0] = dVec[0];
573 >    atomInfo->dipole[1] = dVec[1];
574 >    atomInfo->dipole[2] = dVec[2];
575 >    atomInfo->hasVector = true;
576 >    atomInfo->charge = 3.0;
577 >    atomInfo->hasCharge = true;
578 >    atomData->addAtomInfo(atomInfo);
579 >
580 >    //add atom data into atom's property
581 >
582 >    if(!haveAtomData){
583 >      atomData->setID("ATOMDATA");
584 >      datom->addProperty(atomData);
585 >    }
586 >
587 >    setVisited(datom);
588 >
589 >  }
590 >
591 >  const std::string GBLipidAtomVisitor::toString(){
592 >    char buffer[65535];
593 >    std::string result;
594 >  
595 >    sprintf(buffer ,"------------------------------------------------------------------\n");
596 >    result += buffer;
597 >
598 >    sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
599 >    result += buffer;
600 >
601 >    sprintf(buffer , "Visitor Description: Convert GBlipid into xyz-formatted atom for use with xyz2pov\n");
602 >    result += buffer;
603 >
604 >    sprintf(buffer ,"------------------------------------------------------------------\n");
605 >    result += buffer;
606 >
607 >    return result;
608 >  }
609 >
610 >  bool Ring5gbAtomVisitor::isRing5gbAtom(const std::string& atomType){
611 >    std::set<std::string>::iterator strIter;
612 >    strIter = Ring5gbAtomType.find(atomType);
613 >
614 >    return strIter != Ring5gbAtomType.end() ? true : false;
615 >  }
616 >
617 >  void Ring5gbAtomVisitor::visit(DirectionalAtom* datom){
618 >    std::vector<AtomInfo*> atoms;
619 >    //we need to convert linear into 4 different atoms
620 >    Vector3d c1(0.0, 0.0, -5.5);
621 >    Vector3d c2(0.0, 0.0, -1.8);
622 >    Vector3d c3(0.0, 0.0,  1.8);
623 >    Vector3d c4(0.0, 0.0,  5.5);
624 >    RotMat3x3d rotMatrix;
625 >    RotMat3x3d rotTrans;
626 >    AtomInfo* atomInfo;
627 >    Vector3d pos;
628 >    Vector3d newVec;
629 >    Vector3d dVec;
630 >    Quat4d q;
631 >    AtomData* atomData;
632 >    GenericData* data;
633 >    bool haveAtomData;
634 >
635 >    //if atom is not Ring5GB atom, just skip it
636 >    if(!isRing5gbAtom(datom->getType()))
637 >      return;
638 >
639 >    data = datom->getPropertyByName("ATOMDATA");
640 >    if(data != NULL){
641 >      atomData = dynamic_cast<AtomData*>(data);  
642 >      if(atomData == NULL){
643 >        std::cerr << "can not get Atom Data from " << datom->getType() << std::endl;
644 >        atomData = new AtomData;
645 >        haveAtomData = false;      
646 >      } else {
647 >        haveAtomData = true;
648 >      }
649 >    } else {
650 >      atomData = new AtomData;
651 >      haveAtomData = false;
652 >    }
653 >  
654 >  
655 >    pos = datom->getPos();
656 >    q = datom->getQ();
657 >    rotMatrix = datom->getA();
658 >
659 >    // We need A^T to convert from body-fixed to space-fixed:  
660 >    rotTrans = rotMatrix.transpose();
661 >
662 >    newVec = rotTrans * c1;
663 >    atomInfo = new AtomInfo;
664 >    atomInfo->atomTypeName = "K";
665 >    atomInfo->pos[0] = pos[0] + newVec[0];
666 >    atomInfo->pos[1] = pos[1] + newVec[1];
667 >    atomInfo->pos[2] = pos[2] + newVec[2];
668 >    atomInfo->dipole[0] = 0.0;
669 >    atomInfo->dipole[1] = 0.0;
670 >    atomInfo->dipole[2] = 0.0;
671 >    atomData->addAtomInfo(atomInfo);
672 >
673 >    newVec = rotTrans * c2;
674 >    atomInfo = new AtomInfo;
675 >    atomInfo->atomTypeName = "K";
676 >    atomInfo->pos[0] = pos[0] + newVec[0];
677 >    atomInfo->pos[1] = pos[1] + newVec[1];
678 >    atomInfo->pos[2] = pos[2] + newVec[2];
679 >    atomInfo->dipole[0] = 0.0;
680 >    atomInfo->dipole[1] = 0.0;
681 >    atomInfo->dipole[2] = 0.0;
682 >    atomData->addAtomInfo(atomInfo);
683 >
684 >    newVec = rotTrans * c3;
685 >    atomInfo = new AtomInfo;
686 >    atomInfo->atomTypeName = "K";
687 >    atomInfo->pos[0] = pos[0] + newVec[0];
688 >    atomInfo->pos[1] = pos[1] + newVec[1];
689 >    atomInfo->pos[2] = pos[2] + newVec[2];
690 >    atomInfo->dipole[0] = 0.0;
691 >    atomInfo->dipole[1] = 0.0;
692 >    atomInfo->dipole[2] = 0.0;
693 >    atomData->addAtomInfo(atomInfo);
694 >
695 >    newVec = rotTrans * c4;
696 >    atomInfo = new AtomInfo;
697 >    atomInfo->atomTypeName = "K";
698 >    atomInfo->pos[0] = pos[0] + newVec[0];
699 >    atomInfo->pos[1] = pos[1] + newVec[1];
700 >    atomInfo->pos[2] = pos[2] + newVec[2];
701 >    atomInfo->dipole[0] = 0.0;
702 >    atomInfo->dipole[1] = 0.0;
703 >    atomInfo->dipole[2] = 0.0;
704 >    atomData->addAtomInfo(atomInfo);
705 >
706 >    //add atom data into atom's property
707 >
708 >    if(!haveAtomData){
709 >      atomData->setID("ATOMDATA");
710 >      datom->addProperty(atomData);
711 >    }
712 >
713 >    setVisited(datom);
714 >
715 >  }
716 >
717 >  const std::string Ring5gbAtomVisitor::toString(){
718 >    char buffer[65535];
719 >    std::string result;
720 >  
721 >    sprintf(buffer ,"------------------------------------------------------------------\n");
722 >    result += buffer;
723 >
724 >    sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
725 >    result += buffer;
726 >
727 >    sprintf(buffer , "Visitor Description: Convert Ring5GB into 4 different K atoms\n");
728 >    result += buffer;
729 >
730 >    sprintf(buffer ,"------------------------------------------------------------------\n");
731 >    result += buffer;
732 >
733 >    return result;
734 >  }
735 >
736 >  bool HeadAtomVisitor::isHeadAtom(const std::string& atomType){
737 >    std::set<std::string>::iterator strIter;
738 >    strIter = HeadAtomType.find(atomType);
739 >
740 >    return strIter != HeadAtomType.end() ? true : false;
741 >  }
742 >
743 >  void HeadAtomVisitor::visit(DirectionalAtom* datom){
744 >    std::vector<AtomInfo*> atoms;
745 >    //we need to convert linear into 2 different atoms
746 >    Vector3d c1(0.0, 0.0, -1.5);
747 >    Vector3d c2(0.0, 0.0, 1.5);
748 >    RotMat3x3d rotMatrix;
749 >    RotMat3x3d rotTrans;
750 >    AtomInfo* atomInfo;
751 >    Vector3d pos;
752 >    Vector3d newVec;
753 >    Vector3d dVec;
754 >    Quat4d q;
755 >    AtomData* atomData;
756 >    GenericData* data;
757 >    bool haveAtomData;
758 >
759 >    //if atom is not Head atom, just skip it
760 >    if(!isHeadAtom(datom->getType()))
761 >      return;
762 >
763 >    data = datom->getPropertyByName("ATOMDATA");
764 >    if(data != NULL){
765 >      atomData = dynamic_cast<AtomData*>(data);  
766 >      if(atomData == NULL){
767 >        std::cerr << "can not get Atom Data from " << datom->getType() << std::endl;
768 >        atomData = new AtomData;
769 >        haveAtomData = false;      
770 >      } else {
771 >        haveAtomData = true;
772 >      }
773 >    } else {
774 >      atomData = new AtomData;
775 >      haveAtomData = false;
776 >    }
777 >  
778 >  
779 >    pos = datom->getPos();
780 >    q = datom->getQ();
781 >    rotMatrix = datom->getA();
782 >
783 >    // We need A^T to convert from body-fixed to space-fixed:  
784 >    rotTrans = rotMatrix.transpose();
785 >
786 >    newVec = rotTrans * c1;
787 >    atomInfo = new AtomInfo;
788 >    atomInfo->atomTypeName = "C";
789 >    atomInfo->pos[0] = pos[0] + newVec[0];
790 >    atomInfo->pos[1] = pos[1] + newVec[1];
791 >    atomInfo->pos[2] = pos[2] + newVec[2];
792 >    atomInfo->dipole[0] = 0.0;
793 >    atomInfo->dipole[1] = 0.0;
794 >    atomInfo->dipole[2] = 0.0;
795 >    atomData->addAtomInfo(atomInfo);
796 >
797 >    newVec = rotTrans * c2;
798 >    atomInfo = new AtomInfo;
799 >    atomInfo->atomTypeName = "O";
800 >    atomInfo->pos[0] = pos[0] + newVec[0];
801 >    atomInfo->pos[1] = pos[1] + newVec[1];
802 >    atomInfo->pos[2] = pos[2] + newVec[2];
803 >    atomInfo->dipole[0] = 0.0;
804 >    atomInfo->dipole[1] = 0.0;
805 >    atomInfo->dipole[2] = 0.0;
806 >    atomData->addAtomInfo(atomInfo);
807 >
808 >    //add atom data into atom's property
809 >
810 >    if(!haveAtomData){
811 >      atomData->setID("ATOMDATA");
812 >      datom->addProperty(atomData);
813 >    }
814 >
815 >    setVisited(datom);
816 >
817 >  }
818 >
819 >  const std::string HeadAtomVisitor::toString(){
820 >    char buffer[65535];
821 >    std::string result;
822 >  
823 >    sprintf(buffer ,"------------------------------------------------------------------\n");
824 >    result += buffer;
825 >
826 >    sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
827 >    result += buffer;
828 >
829 >    sprintf(buffer , "Visitor Description: Convert HEAD into C atom and O atom\n");
830 >    result += buffer;
831 >
832 >    sprintf(buffer ,"------------------------------------------------------------------\n");
833 >    result += buffer;
834 >
835 >    return result;
836 >  }
837 >
838 >
839 >  //----------------------------------------------------------------------------//
840 >
841 >  void DefaultAtomVisitor::visit(Atom *atom) {
842      AtomData *atomData;
843      AtomInfo *atomInfo;
844      Vector3d  pos;
845  
846      if (isVisited(atom))
847 <        return;
847 >      return;
848  
849      atomInfo = new AtomInfo;
850  
# Line 368 | Line 865 | void DefaultAtomVisitor::visit(Atom *atom) {
865      atom->addProperty(atomData);
866  
867      setVisited(atom);
868 < }
868 >  }
869  
870 < void DefaultAtomVisitor::visit(DirectionalAtom *datom) {
870 >  void DefaultAtomVisitor::visit(DirectionalAtom *datom) {
871      AtomData *atomData;
872      AtomInfo *atomInfo;
873      Vector3d  pos;
874      Vector3d  u;
875  
876      if (isVisited(datom))
877 <        return;
877 >      return;
878  
879      pos = datom->getPos();
880 <    u = datom->getElectroFrame().getColumn(2);
881 <
880 >    if (datom->getAtomType()->isGayBerne()) {
881 >        u = datom->getA().transpose()*V3Z;        
882 >    } else if (datom->getAtomType()->isMultipole()) {
883 >        u = datom->getElectroFrame().getColumn(2);
884 >    }
885      atomData = new AtomData;
886      atomData->setID("ATOMDATA");
887      atomInfo = new AtomInfo;
# Line 399 | Line 899 | void DefaultAtomVisitor::visit(DirectionalAtom *datom)
899      datom->addProperty(atomData);
900  
901      setVisited(datom);
902 < }
902 >  }
903  
904 < const std::string DefaultAtomVisitor::toString() {
904 >  const std::string DefaultAtomVisitor::toString() {
905      char   buffer[65535];
906      std::string result;
907  
# Line 421 | Line 921 | const std::string DefaultAtomVisitor::toString() {
921      result += buffer;
922  
923      return result;
924 < }
924 >  }
925   } //namespace oopse

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